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- PDB-6ftr: Serial Femtosecond Crystallography at Megahertz pulse rates -

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Basic information

Entry
Database: PDB / ID: 6ftr
TitleSerial Femtosecond Crystallography at Megahertz pulse rates
ComponentsLysozyme C
KeywordsHYDROLASE / XFEL / serial crystallography / SFX / European XFEL
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.76000104975 Å
AuthorsWiedorn, M.O. / Oberthuer, D. / Barty, A. / Chapman, H.N.
CitationJournal: Nat Commun / Year: 2018
Title: Megahertz serial crystallography.
Authors: Wiedorn, M.O. / Oberthur, D. / Bean, R. / Schubert, R. / Werner, N. / Abbey, B. / Aepfelbacher, M. / Adriano, L. / Allahgholi, A. / Al-Qudami, N. / Andreasson, J. / Aplin, S. / Awel, S. / ...Authors: Wiedorn, M.O. / Oberthur, D. / Bean, R. / Schubert, R. / Werner, N. / Abbey, B. / Aepfelbacher, M. / Adriano, L. / Allahgholi, A. / Al-Qudami, N. / Andreasson, J. / Aplin, S. / Awel, S. / Ayyer, K. / Bajt, S. / Barak, I. / Bari, S. / Bielecki, J. / Botha, S. / Boukhelef, D. / Brehm, W. / Brockhauser, S. / Cheviakov, I. / Coleman, M.A. / Cruz-Mazo, F. / Danilevski, C. / Darmanin, C. / Doak, R.B. / Domaracky, M. / Dorner, K. / Du, Y. / Fangohr, H. / Fleckenstein, H. / Frank, M. / Fromme, P. / Ganan-Calvo, A.M. / Gevorkov, Y. / Giewekemeyer, K. / Ginn, H.M. / Graafsma, H. / Graceffa, R. / Greiffenberg, D. / Gumprecht, L. / Gottlicher, P. / Hajdu, J. / Hauf, S. / Heymann, M. / Holmes, S. / Horke, D.A. / Hunter, M.S. / Imlau, S. / Kaukher, A. / Kim, Y. / Klyuev, A. / Knoska, J. / Kobe, B. / Kuhn, M. / Kupitz, C. / Kupper, J. / Lahey-Rudolph, J.M. / Laurus, T. / Le Cong, K. / Letrun, R. / Xavier, P.L. / Maia, L. / Maia, F.R.N.C. / Mariani, V. / Messerschmidt, M. / Metz, M. / Mezza, D. / Michelat, T. / Mills, G. / Monteiro, D.C.F. / Morgan, A. / Muhlig, K. / Munke, A. / Munnich, A. / Nette, J. / Nugent, K.A. / Nuguid, T. / Orville, A.M. / Pandey, S. / Pena, G. / Villanueva-Perez, P. / Poehlsen, J. / Previtali, G. / Redecke, L. / Riekehr, W.M. / Rohde, H. / Round, A. / Safenreiter, T. / Sarrou, I. / Sato, T. / Schmidt, M. / Schmitt, B. / Schonherr, R. / Schulz, J. / Sellberg, J.A. / Seibert, M.M. / Seuring, C. / Shelby, M.L. / Shoeman, R.L. / Sikorski, M. / Silenzi, A. / Stan, C.A. / Shi, X. / Stern, S. / Sztuk-Dambietz, J. / Szuba, J. / Tolstikova, A. / Trebbin, M. / Trunk, U. / Vagovic, P. / Ve, T. / Weinhausen, B. / White, T.A. / Wrona, K. / Xu, C. / Yefanov, O. / Zatsepin, N. / Zhang, J. / Perbandt, M. / Mancuso, A.P. / Betzel, C. / Chapman, H. / Barty, A.
History
DepositionFeb 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: diffrn / entity
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight
Revision 1.3Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,85311
Polymers14,3311
Non-polymers52210
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-19 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.300, 79.300, 37.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-355-

HOH

31A-379-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 91 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 3.5
Details: NaCl, ethylene glycol, PEG 3350, acetate buffer pH 3.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3332 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3332 Å / Relative weight: 1
ReflectionResolution: 1.76→22 Å / Num. obs: 12387 / % possible obs: 99.64 % / Redundancy: 133.725 % / Biso Wilson estimate: 26.18 Å2 / CC1/2: 0.98 / R split: 0.1041 / Net I/σ(I): 7.27
Reflection shellResolution: 1.76→1.823 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.43 / Num. unique obs: 582 / CC1/2: 0.7 / R split: 0.4605 / % possible all: 95.88

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4et9

4et9


Resolution: 1.76000104975→21.9938627803 Å / SU ML: 0.153685891609 / Cross valid method: FREE R-VALUE / σ(F): 1.34754767684 / Phase error: 16.7038461173
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.173067705247 1220 9.85301243741 %Random selection
Rwork0.155289922729 11162 --
obs0.157027336738 12382 99.7181283724 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.8819367849 Å2
Refinement stepCycle: LAST / Resolution: 1.76000104975→21.9938627803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 31 81 1113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0100315959411192
X-RAY DIFFRACTIONf_angle_d1.077979889551615
X-RAY DIFFRACTIONf_chiral_restr0.0607569629013159
X-RAY DIFFRACTIONf_plane_restr0.00581969572473221
X-RAY DIFFRACTIONf_dihedral_angle_d13.7574484305719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.83040.2220071799771290.2051738459791178X-RAY DIFFRACTION97.4645786726
1.8304-1.91370.2496413139351330.1790642317181217X-RAY DIFFRACTION99.925980755
1.9137-2.01450.2136155057681340.1566378869111213X-RAY DIFFRACTION100
2.0145-2.14060.190898638771320.1427039904431228X-RAY DIFFRACTION100
2.1406-2.30580.1511352152061360.1388926914871222X-RAY DIFFRACTION100
2.3058-2.53750.1669036082861340.141490015021237X-RAY DIFFRACTION100
2.5375-2.9040.189465377551360.1453498569161253X-RAY DIFFRACTION100
2.904-3.6560.1553073054211390.1466552688331264X-RAY DIFFRACTION100
3.656-21.99560.1640281884781470.168032322141350X-RAY DIFFRACTION100

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